Beyond Sequence: Internucleosomal Interactions Dominate Array Assembly

Abstract

The organization of the nucleosome array is a critical component of the chromatin assembly into higher order structure as well as its function. Here, we investigated the contributions of the DNA sequence and internucleosomal interactions on the organization of the nucleosomal arrays in compact structures using atomic force microscopy. We assembled nucleosomes on DNA substrates allowing for the formation of tetranucleosomes. We found that nucleosomes are capable of close positioning with no discernible space between them, even in the case of assembled dinucleosomes. This morphology of the array is in contrast with that observed for arrays assembled with repeats of the nucleosome positioning motifs separated by uniform spacers. Simulated assembly of tetranucleosomes by random placement along the substrates revealed that nucleosome array compaction is promoted by the interaction of the nucleosomes. We developed a theoretical model to account for the role of DNA sequence and internucleosomal interactions in the formation of the nucleosome structures. These findings suggest that, in the chromatin assembly, the affinity of the nucleosomes to the DNA sequence and the strengths of the internucleosomal interactions are the two major factors defining the compactness of the chromatin.

Nanoscale Structure, Interactions, and Dynamics of Centromere Nucleosomes

“…2), the nucleosome can be seen to be overwrapped. These data show that there was a partial unwrapping event that started in frame (11) and proceeded to frame (13), where the nucleosome went from a state of overwrapped (~210 bp) and, throughout three frames, it decreased to an under wrapped state (~100 bp), where it remained bound for another 7 frames. The last frame 29 shows the nucleosome wholly disassociated from the DNA.…”

“…We have demonstrated that the balance between energies of internucleosomal interaction and the affinity of the nucleosome core to the DNA sequence previously defines the formation of tight contacts between the nucleosomes. 10,13 The balance favors the dinucleosome assembly for non-specific DNA sequences. We have shown that the number of such contacts increases in nucleosomes assembled with truncated H4 histone, suggesting that histone tails contribute to the tightening of dinucleosomes.…”

“…5 We used DNA templates with different sequences and AFM visualization to directly characterize the role of the DNA sequence on the positioning of nucleosomes and their interactions. 5,[9][10][11][12][13] In paper 13 , we used DNA templates with different sequences and found that nucleosomes are capable of close positioning with no discernible space between them, even in the case of assembled dinucleosomes. This array morphology contrasts with that observed for arrays assembled with repeats of the nucleosome positioning motifs separated by uniform spacers.…”

The Interaction of NF-κB Transcription Factor with Centromeric Chromatin

“…Elevated stability of the nucleosome assembled by the specific 601 DNA sequence can explain this effect 37 . Still, we need to consider the difference in the interaction of NF-κB with both DNA templates.…”

“…However, nucleosomes were assembled on the highly specific 601 sequence in that publication, and a lower unwrapping effect was observed. Elevated stability of the nucleosome assembled by the specific 601 DNA sequence can explain this effect 37 . Still, we need to consider the difference in the interaction of NF-κB with both DNA templates.…”